I've been using Xubuntu 9.04 for a week or so (apologies, but I am a Gnome Mint user too and the old Xubuntu forum has vanished). As of a few hours ago, each time I boot up, when restarting or from the machine being off, I get the settings manager there on the screen. There is no listing for it in Session & Startup.

The only thing I can think of is that it relates to some work I did on a theme while in root. But I don't exactly know how or what or what I do to reverse this.

"It's probably listed in the session cache. You could try running 'rm -f ~/.cache/sessions/*' from a console when logged out from X entirely. Alternatively, you could open the 'Session and Startup' panel, select the 'Session' tab, and clock 'Save Session' to write the current session information to the cache. I find the other method more reliable, though."